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Suleman M, Sayaf AM, Aftab S, Alissa M, Alghamdi A, Alghamdi SA, Alshehri MA, Yeoh KK, Crovella S, Shaito AA. Medicinal Phytocompounds as Potential Inhibitors of p300-HIF1α Interaction: A Structure-Based Screening and Molecular Dynamics Simulation Study. Pharmaceuticals (Basel) 2025; 18:602. [PMID: 40284037 PMCID: PMC12030413 DOI: 10.3390/ph18040602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2025] [Revised: 04/09/2025] [Accepted: 04/15/2025] [Indexed: 04/29/2025] Open
Abstract
Background: Hypoxia plays a key role in cancer progression, mainly by stabilizing and activating hypoxia-inducible factor-1 (HIF-1). For HIF-1 to function under low oxygen conditions, it must interact with the transcriptional coactivator p300, a critical step for promoting cancer cell survival and adaptation in hypoxic environments. Methods: Consequently, we used drug design and molecular simulation techniques to screen phytochemical databases, including traditional Chinese and African medicine sources, for compounds that could disrupt the p300/HIF-1 interaction. Results: In this study, we identified potential compounds with high docking scores such as EA-176920 (-8.719), EA-46881231 (-8.642), SA-31161 (-9.580), SA-5280863 (-8.179), NE-5280362 (-10.287), NE-72276 (-9.017), NA-11210533 (-10.366), NA-11336960 (-7.818), TCM-5281792 (-12.648), and TCM-6441280 (-9.470 kcal/mol) as lead compounds. Furthermore, the compound with the highest docking score from each database (EA-176920, SA-31161, NE-5280362, NA-11210533, and TCM-5281792) was subjected to further analysis. The stable binding affinity of these compounds with p300 was confirmed by Post-simulation binding free energy (-22.0020 kcal/mol, -25.4499 kcal/mol, -32.4530 kcal/mol, -33.9918 kcal/mol, and -57.7755 kcal/mol, respectively) and KD analysis. Moreover, the selected compounds followed the Lipinski rules with favorable ADMET properties like efficient intestinal absorption, high water solubility, and no toxicity. Conclusions: Our findings highlight the potential of natural compounds to target key protein-protein interactions in cancer and lay the groundwork for future in vitro and in vivo studies to explore their therapeutic potential. Specifically, disrupting the p300/HIF-1 interaction could interfere with hypoxia-driven pathways that promote tumor growth, angiogenesis, and metastasis, offering a promising strategy to suppress cancer progression at the molecular level.
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Affiliation(s)
- Muhammad Suleman
- Laboratory of Animal Research Center (LARC), Qatar University, Doha P.O. Box 2713, Qatar;
- Center for Biotechnology and Microbiology, University of Swat, Swat 19200, Pakistan;
| | - Abrar Mohammad Sayaf
- School of Chemical Sciences, Universiti Sains Malaysia, Gelugor 10050, Penang, Malaysia; (A.M.S.); (K.K.Y.)
| | - Sohail Aftab
- Center for Biotechnology and Microbiology, University of Swat, Swat 19200, Pakistan;
| | - Mohammed Alissa
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia; (M.A.); (A.A.); (S.A.A.); (M.A.A.)
| | - Abdullah Alghamdi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia; (M.A.); (A.A.); (S.A.A.); (M.A.A.)
| | - Suad A. Alghamdi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia; (M.A.); (A.A.); (S.A.A.); (M.A.A.)
| | - Mohammed A. Alshehri
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia; (M.A.); (A.A.); (S.A.A.); (M.A.A.)
| | - Kar Kheng Yeoh
- School of Chemical Sciences, Universiti Sains Malaysia, Gelugor 10050, Penang, Malaysia; (A.M.S.); (K.K.Y.)
| | - Sergio Crovella
- Laboratory of Animal Research Center (LARC), Qatar University, Doha P.O. Box 2713, Qatar;
| | - Abdullah A. Shaito
- Biomedical Research Center (BRC), Department of Biomedical Sciences at College of Health Sciences, and College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar
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Majerciak V, Alvarado-Hernandez B, Ma Y, Duduskar S, Lobanov A, Cam M, Zheng ZM. A KSHV RNA-binding protein promotes FOS to inhibit nuclease AEN and transactivate RGS2 for AKT phosphorylation. mBio 2025; 16:e0317224. [PMID: 39655935 PMCID: PMC11708059 DOI: 10.1128/mbio.03172-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Accepted: 10/30/2024] [Indexed: 12/18/2024] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) encodes an RNA-binding protein ORF57 in lytic infection. Using an optimized CLIP-seq in this report, we identified ORF57-bound transcripts from 544 host protein-coding genes. By comparing with the RNA-seq profiles from BCBL-1 cells with latent and lytic KSHV infection and from HEK293T cells with and without ORF57 expression, we identified FOS RNA as one of the major ORF57-specific RNA targets. FOS dimerizes with JUN as a transcription factor AP-1 involved in cell proliferation, differentiation, and transformation. Knockout of the ORF57 gene from the KSHV genome led BAC16-iSLK cells incapable of FOS expression in KSHV lytic infection. The dysfunctional KSHV genome in FOS expression could be rescued by Lenti-ORF57 virus infection. ORF57 protein does not regulate FOS translation but binds to the 13-nt RNA motif near the FOS RNA 5' end and prolongs FOS mRNA half-life 7.7 times longer than it is in the absence of ORF57. This binding of ORF57 to FOS RNA is likely competitive to the binding of host nuclease AEN (ISG20L1) of which physiological RNase activity remains unknown. KSHV infection inhibits the expression of AEN, but not exosomal RNA helicase MTR4. FOS expression mediated by ORF57 inhibits AEN transcription through FOS binding to AEN promoter but transactivates RGS2, a regulator of G-protein-coupled receptors. FOS binds a conserved AP-1 site in the RGS2 promoter and enhances RGS2 expression to phosphorylate AKT. Altogether, we have discovered that KSHV ORF57 specifically binds and stabilizes FOS RNA to increase FOS expression, thereby disturbing host gene expression and inducing pathogenesis during KSHV lytic infection.IMPORTANCEWe discovered that FOS, a heterodimer component of oncogenic transcription factor AP-1, is highly elevated in KSHV-infected cells by expression of a viral lytic RNA-binding protein, ORF57, which binds a 13-nt RNA motif near the FOS RNA 5' end to prolong FOS RNA half-life. This binding of ORF57 to FOS RNA is competitive to the binding of host RNA destabilizer(s). KSHV infection inhibits expression of host nuclease AEN, but not MTR4. FOS inhibits AEN transcription by binding to the AEN promoter but transactivates RGS2 by binding to a conserved AP-1 site in the RGS2 promoter, thereby enhancing RGS2 expression and phosphorylation of AKT. Thus, KSHV lytic infection controls the expression of a subset of genes for signaling, cell cycle progression, and proliferation to potentially contribute to viral oncogenesis.
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Affiliation(s)
- Vladimir Majerciak
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, NCI/NIH, Frederick, Maryland, USA
| | - Beatriz Alvarado-Hernandez
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, NCI/NIH, Frederick, Maryland, USA
| | - Yanping Ma
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, NCI/NIH, Frederick, Maryland, USA
| | - Shivalee Duduskar
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, NCI/NIH, Frederick, Maryland, USA
| | - Alexei Lobanov
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, NCI/NIH, Bethesda, Maryland, USA
| | - Maggie Cam
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, NCI/NIH, Bethesda, Maryland, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, NCI/NIH, Frederick, Maryland, USA
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3
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Karunatilleke NC, Brickenden A, Choy WY. Molecular basis of the interactions between the disordered Neh4 and Neh5 domains of Nrf2 and CBP/p300 in oxidative stress response. Protein Sci 2024; 33:e5137. [PMID: 39150085 PMCID: PMC11328122 DOI: 10.1002/pro.5137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/21/2024] [Accepted: 07/22/2024] [Indexed: 08/17/2024]
Abstract
Nuclear factor erythroid 2-related factor 2 (Nrf2) is a major transcription factor that functions in maintaining redox homeostasis in cells. It mediates the transcription of cytoprotective genes in response to environmental and endogenous stresses to prevent oxidative damage. Thus, Nrf2 plays a significant role in chemoprevention. However, aberrant activation of Nrf2 has been shown to protect cancer cells from apoptosis and contribute to their chemoresistance. The interaction between Nrf2 and CBP is critical for the gene transcription activation. CBP and its homologue p300 interact with two transactivation domains in Nrf2, Neh4, and Neh5 domains through their TAZ1 and TAZ2 domains. To date, the molecular basis of this crucial interaction is not known, hindering a more detailed understanding of the regulation of Nrf2. To close this knowledge gap, we have used a set of biophysical experiments to dissect the Nrf2-CBP/p300 interactions. Structural properties of Neh4 and Neh5 and their binding with the TAZ1 and TAZ2 domains of CBP/p300 were characterized. Our results show that the Neh4 and Neh5 domains of Nrf2 are intrinsically disordered, and they both can bind the TAZ1 and TAZ2 domains of CBP/p300 with micromolar affinities. The findings provide molecular insight into the regulation of Nrf2 by CBP/p300 through multi-domain interactions.
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Affiliation(s)
- Nadun C Karunatilleke
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Anne Brickenden
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
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Kuna M, Soares MJ. Cited2 is a key regulator of placental development and plasticity. Bioessays 2024; 46:e2300118. [PMID: 38922923 PMCID: PMC11331489 DOI: 10.1002/bies.202300118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
The biology of trophoblast cell lineage development and placentation is characterized by the involvement of several known transcription factors. Central to the action of a subset of these transcriptional regulators is CBP-p300 interacting transactivator with Glu/Asp-rich carboxy-terminal domain 2 (CITED2). CITED2 acts as a coregulator modulating transcription factor activities and affecting placental development and adaptations to physiological stressors. These actions of CITED2 on the trophoblast cell lineage and placentation are conserved across the mouse, rat, and human. Thus, aspects of CITED2 biology in hemochorial placentation can be effectively modeled in the mouse and rat. In this review, we present information on the conserved role of CITED2 in the biology of placentation and discuss the use of CITED2 as a tool to discover new insights into regulatory mechanisms controlling placental development.
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Affiliation(s)
- Marija Kuna
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS
| | - Michael J. Soares
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS
- Center for Perinatal Research, Children’s Mercy Research Institute, Children’s Mercy, Kansas City, MO
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5
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Petrovicz VL, Pasztuhov I, Martinek TA, Hegedüs Z. Site-directed allostery perturbation to probe the negative regulation of hypoxia inducible factor-1α. RSC Chem Biol 2024; 5:711-720. [PMID: 39092442 PMCID: PMC11289882 DOI: 10.1039/d4cb00066h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/27/2024] [Indexed: 08/04/2024] Open
Abstract
The interaction between the intrinsically disordered transcription factor HIF-1α and the coactivator proteins p300/CBP is essential in the fast response to low oxygenation. The negative feedback regulator, CITED2, switches off the hypoxic response through a very efficient irreversible mechanism. The negative cooperativity with HIF-1α relies on the formation of a ternary intermediate that leads to allosteric structural changes in p300/CBP, in which the cooperative folding/binding of the CITED2 sequence motifs plays a key role. Understanding the contribution of a binding motif to the structural changes in relation to competition efficiency provides invaluable insights into the molecular mechanism. Our strategy is to site-directedly perturb the p300-CITED2 complex's structure without significantly affecting binding thermodynamics. In this way, the contribution of a sequence motif to the negative cooperativity with HIF-1α would mainly depend on the induced structural changes, and to a lesser extent on binding affinity. Using biophysical assays and NMR measurements, we show here that the interplay between the N-terminal tail and the rest of the binding motifs of CITED2 is crucial for the unidirectional displacement of HIF-1α. We introduce an advantageous approach for evaluating the roles of the different sequence parts with the help of motif-by-motif backbone perturbations.
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Affiliation(s)
- Vencel L Petrovicz
- University of Szeged, Department of Medical Chemistry 8 Dóm tér Szeged 6720 Hungary
| | - István Pasztuhov
- University of Szeged, Department of Medical Chemistry 8 Dóm tér Szeged 6720 Hungary
| | - Tamás A Martinek
- University of Szeged, Department of Medical Chemistry 8 Dóm tér Szeged 6720 Hungary
- HUN-REN SZTE Biomimetic Systems Research Group 8 Dóm tér Szeged 6720 Hungary
| | - Zsófia Hegedüs
- University of Szeged, Department of Medical Chemistry 8 Dóm tér Szeged 6720 Hungary
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Jacquemin C, El Orch W, Diaz O, Lalande A, Aublin-Gex A, Jacolin F, Toesca J, Si-Tahar M, Mathieu C, Lotteau V, Perrin-Cocon L, Vidalain PO. Pharmacological induction of the hypoxia response pathway in Huh7 hepatoma cells limits proliferation but increases resilience under metabolic stress. Cell Mol Life Sci 2024; 81:320. [PMID: 39078527 PMCID: PMC11335246 DOI: 10.1007/s00018-024-05361-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/25/2024] [Accepted: 07/12/2024] [Indexed: 07/31/2024]
Abstract
The hypoxia response pathway enables adaptation to oxygen deprivation. It is mediated by hypoxia-inducible factors (HIF), which promote metabolic reprogramming, erythropoiesis, angiogenesis and tissue remodeling. This led to the successful development of HIF-inducing drugs for treating anemia and some of these molecules are now in clinic. However, elevated levels of HIFs are frequently associated with tumor growth, poor prognosis, and drug resistance in various cancers, including hepatocellular carcinoma (HCC). Consequently, there are concerns regarding the recommendation of HIF-inducing drugs in certain clinical situations. Here, we analyzed the effects of two HIF-inducing drugs, Molidustat and Roxadustat, in the well-characterized HCC cell line Huh7. These drugs increased HIF-1α and HIF-2α protein levels which both participate in inducing hypoxia response genes such as BNIP3, SERPINE1, LDHA or EPO. Combined transcriptomics, proteomics and metabolomics showed that Molidustat increased the expression of glycolytic enzymes, while the mitochondrial network was fragmented and cellular respiration decreased. This metabolic remodeling was associated with a reduced proliferation and a lower demand for pyrimidine supply, but an increased ability of cells to convert pyruvate to lactate. This was accompanied by a higher resistance to the inhibition of mitochondrial respiration by antimycin A, a phenotype confirmed in Roxadustat-treated Huh7 cells and Molidustat-treated hepatoblastoma cells (Huh6 and HepG2). Overall, this study shows that HIF-inducing drugs increase the metabolic resilience of liver cancer cells to metabolic stressors, arguing for careful monitoring of patients treated with HIF-inducing drugs, especially when they are at risk of liver cancer.
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Affiliation(s)
- Clémence Jacquemin
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France
| | - Walid El Orch
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France
| | - Olivier Diaz
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France
| | - Alexandre Lalande
- CIRI, Centre International de Recherche en Infectiologie, Team NeuroInvasion, Tropism and Viral Encephalitis, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France
| | - Anne Aublin-Gex
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France
| | - Florentine Jacolin
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France
| | - Johan Toesca
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France
| | - Mustapha Si-Tahar
- Centre d'Etude des Pathologies Respiratoires (CEPR), Faculty of Medecine, Inserm, U1100, 37000, Tours, France
| | - Cyrille Mathieu
- CIRI, Centre International de Recherche en Infectiologie, Team NeuroInvasion, Tropism and Viral Encephalitis, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France
| | - Vincent Lotteau
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France
- Laboratoire P4 INSERM-Jean Mérieux, Lyon, France
| | - Laure Perrin-Cocon
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France.
| | - Pierre-Olivier Vidalain
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France.
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Wiggins DA, Maxwell JN, Nelson DE. Exploring the role of CITED transcriptional regulators in the control of macrophage polarization. Front Immunol 2024; 15:1365718. [PMID: 38646545 PMCID: PMC11032013 DOI: 10.3389/fimmu.2024.1365718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Macrophages are tissue resident innate phagocytic cells that take on contrasting phenotypes, or polarization states, in response to the changing combination of microbial and cytokine signals at sites of infection. During the opening stages of an infection, macrophages adopt the proinflammatory, highly antimicrobial M1 state, later shifting to an anti-inflammatory, pro-tissue repair M2 state as the infection resolves. The changes in gene expression underlying these transitions are primarily governed by nuclear factor kappaB (NF-κB), Janus kinase (JAK)/signal transducer and activation of transcription (STAT), and hypoxia-inducible factor 1 (HIF1) transcription factors, the activity of which must be carefully controlled to ensure an effective yet spatially and temporally restricted inflammatory response. While much of this control is provided by pathway-specific feedback loops, recent work has shown that the transcriptional co-regulators of the CBP/p300-interacting transactivator with glutamic acid/aspartic acid-rich carboxy-terminal domain (CITED) family serve as common controllers for these pathways. In this review, we describe how CITED proteins regulate polarization-associated gene expression changes by controlling the ability of transcription factors to form chromatin complexes with the histone acetyltransferase, CBP/p300. We will also cover how differences in the interactions between CITED1 and 2 with CBP/p300 drive their contrasting effects on pro-inflammatory gene expression.
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Affiliation(s)
| | | | - David E. Nelson
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, United States
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Sipko EL, Chappell GF, Berlow RB. Multivalency emerges as a common feature of intrinsically disordered protein interactions. Curr Opin Struct Biol 2024; 84:102742. [PMID: 38096754 DOI: 10.1016/j.sbi.2023.102742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 02/09/2024]
Abstract
Intrinsically disordered proteins (IDPs) use their unique molecular properties and conformational plasticity to interact with cellular partners in a wide variety of biological contexts. Multivalency is an important feature of IDPs that allows for utilization of an expanded toolkit for interactions with other macromolecules and confers additional complexity to molecular recognition processes. Recent studies have offered insights into how multivalent interactions of IDPs enable responsive and sensitive regulation in the context of transcription and cellular signaling. Multivalency is also widely recognized as an important feature of IDP interactions that mediate formation of biomolecular condensates. We highlight recent examples of multivalent interactions of IDPs across diverse contexts to illustrate the breadth of biological processes that utilize multivalency in molecular interactions.
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Affiliation(s)
- Emily L Sipko
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Garrett F Chappell
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rebecca B Berlow
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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9
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Majerciak V, Alvarado-Hernandez B, Ma Y, Duduskar S, Lobanov A, Cam M, Zheng ZM. KSHV promotes oncogenic FOS to inhibit nuclease AEN and transactivate RGS2 for AKT phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.27.577582. [PMID: 38410462 PMCID: PMC10896338 DOI: 10.1101/2024.01.27.577582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 is a lytic RNA-binding protein. We applied BCBL-1 cells in lytic KSHV infection and performed UV cross-linking immunoprecipitation (CLIP) followed by RNA-seq of the CLIPed RNA fragments (CLIP-seq). We identified ORF57-bound transcripts from 544 host protein-coding genes. By comparing with the RNA-seq profiles from BCBL-1 cells with latent and lytic KSHV infection and from HEK293T cells with and without ORF57 expression, we identified FOS and CITED2 RNAs being two common ORF57-specific RNA targets. FOS dimerizes with JUN as a transcription factor AP-1 involved in cell proliferation, differentiation, and transformation. Knockout of the ORF57 gene from the KSHV genome led BAC16-iSLK cells incapable of FOS expression in KSHV lytic infection. The dysfunctional KSHV genome in FOS expression could be rescued by Lenti-ORF57 virus infection. ORF57 protein does not regulate FOS translation but binds to the 13-nt RNA motif near the FOS RNA 5' end and prolongs FOS mRNA half-life 7.7 times longer than it is in the absence of ORF57. This binding of ORF57 to FOS RNA is competitive to the binding of a host nuclease AEN (also referred to as ISG20L1). KSHV infection inhibits the expression of AEN, but not exosomal RNA helicase MTR4. FOS expression mediated by ORF57 inhibits AEN transcription, but transactivates RGS2, a regulator of G-protein coupled receptors. FOS binds a conserved AP-1 site in the RGS2 promoter and enhances RGS2 expression to phosphorylate AKT. Altogether, we have discovered that KSHV ORF57 specifically binds and stabilizes FOS RNA to increase FOS expression, thereby disturbing host gene expression and inducing pathogenesis during KSHV lytic infection.
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Affiliation(s)
- Vladimir Majerciak
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, NCI/NIH, Frederick, MD, 21702, USA
| | - Beatriz Alvarado-Hernandez
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, NCI/NIH, Frederick, MD, 21702, USA
| | - Yanping Ma
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, NCI/NIH, Frederick, MD, 21702, USA
| | - Shivalee Duduskar
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, NCI/NIH, Frederick, MD, 21702, USA
| | - Alexei Lobanov
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, NCI/NIH, Bethesda, MD, 20892, USA
| | - Maggie Cam
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, NCI/NIH, Bethesda, MD, 20892, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, NCI/NIH, Frederick, MD, 21702, USA
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10
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Kotha SR, Staller MV. Clusters of acidic and hydrophobic residues can predict acidic transcriptional activation domains from protein sequence. Genetics 2023; 225:iyad131. [PMID: 37462277 PMCID: PMC10550315 DOI: 10.1093/genetics/iyad131] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/03/2023] [Indexed: 10/06/2023] Open
Abstract
Transcription factors activate gene expression in development, homeostasis, and stress with DNA binding domains and activation domains. Although there exist excellent computational models for predicting DNA binding domains from protein sequence, models for predicting activation domains from protein sequence have lagged, particularly in metazoans. We recently developed a simple and accurate predictor of acidic activation domains on human transcription factors. Here, we show how the accuracy of this human predictor arises from the clustering of aromatic, leucine, and acidic residues, which together are necessary for acidic activation domain function. When we combine our predictor with the predictions of convolutional neural network (CNN) models trained in yeast, the intersection is more accurate than individual models, emphasizing that each approach carries orthogonal information. We synthesize these findings into a new set of activation domain predictions on human transcription factors.
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Affiliation(s)
- Sanjana R Kotha
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Center for Computational Biology, University of California, Berkeley, CA 94720, USA
| | - Max Valentín Staller
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Center for Computational Biology, University of California, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
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11
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Swamynathan SK, Swamynathan S. Corneal epithelial development and homeostasis. Differentiation 2023; 132:4-14. [PMID: 36870804 PMCID: PMC10363238 DOI: 10.1016/j.diff.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/27/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023]
Abstract
The corneal epithelium (CE), the most anterior cellular structure of the eye, is a self-renewing stratified squamous tissue that protects the rest of the eye from external elements. Each cell in this exquisite three-dimensional structure needs to have proper polarity and positional awareness for the CE to serve as a transparent, refractive, and protective tissue. Recent studies have begun to elucidate the molecular and cellular events involved in the embryonic development, post-natal maturation, and homeostasis of the CE, and how they are regulated by a well-coordinated network of transcription factors. This review summarizes the status of related knowledge and aims to provide insight into the pathophysiology of disorders caused by disruption of CE development, and/or homeostasis.
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Affiliation(s)
| | - Sudha Swamynathan
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
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12
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Wen ML, Wu P, Jiang WD, Liu Y, Wu CM, Zhong CB, Li SW, Tang L, Feng L, Zhou XQ. Dietary threonine improves muscle nutritional value and muscle hardness associated with collagen synthesis in grass carp (Ctenopharyngodon idella). Food Chem 2023; 422:136223. [PMID: 37121206 DOI: 10.1016/j.foodchem.2023.136223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/02/2023]
Abstract
To further explain the improvement effect of threonine (Thr) on the fillet quality of fish, a 9-week feeding experiment was conducted. After feeding graded levels of Thr (2.38, 5.38, 8.38, 11.38, 14.38 and 17.38 g/kg), the compositions of fillet hydrolyzed amino acid and fatty acid, and the muscle hardness associated with collagen biosynthesis were mainly analyzed in grass carp (Ctenopharyngodon idella). The results showed that Thr increased the pH value, changed the amino acids and fatty acid composition of fillets, especially essential amino acid (EAA), C22:6n3 (DHA) and C20:5n3 (EPA). Furthermore, this study revealed for the first time that the improvement of muscle hardness by Thr was associated with collagen biosynthesis, and the TGF-β1/Smads, LARP6a and Hsp47 regulate transcriptional processes, translation initiation and post-translational modifications in collagen biosynthesis, respectively. This study offered a basis for exploring the contribution of Thr in improving muscle quality in sub-adult grass carp.
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Affiliation(s)
- Mei-Lan Wen
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Pei Wu
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Ministry of Agriculture and Rural Affairs, Key Laboratory of Sichuan Province, Sichuan 611130, China
| | - Wei-Dan Jiang
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Ministry of Agriculture and Rural Affairs, Key Laboratory of Sichuan Province, Sichuan 611130, China
| | - Yang Liu
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Ministry of Agriculture and Rural Affairs, Key Laboratory of Sichuan Province, Sichuan 611130, China
| | - Cai-Mei Wu
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Cheng-Bo Zhong
- Animal Nutrition Institute, Sichuan Academy of Animal Science, Sichuan Animtech Feed Co. Ltd, Chengdu 610066, Sichuan, China
| | - Shu-Wei Li
- Animal Nutrition Institute, Sichuan Academy of Animal Science, Sichuan Animtech Feed Co. Ltd, Chengdu 610066, Sichuan, China
| | - Ling Tang
- Animal Nutrition Institute, Sichuan Academy of Animal Science, Sichuan Animtech Feed Co. Ltd, Chengdu 610066, Sichuan, China
| | - Lin Feng
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Ministry of Agriculture and Rural Affairs, Key Laboratory of Sichuan Province, Sichuan 611130, China.
| | - Xiao-Qiu Zhou
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Ministry of Agriculture and Rural Affairs, Key Laboratory of Sichuan Province, Sichuan 611130, China.
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13
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Jeknić S, Kudo T, Song JJ, Covert MW. An optimized reporter of the transcription factor hypoxia-inducible factor 1α reveals complex HIF-1α activation dynamics in single cells. J Biol Chem 2023; 299:104599. [PMID: 36907438 PMCID: PMC10124923 DOI: 10.1016/j.jbc.2023.104599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/08/2023] [Accepted: 02/20/2023] [Indexed: 03/13/2023] Open
Abstract
Immune cells adopt a variety of metabolic states to support their many biological functions, which include fighting pathogens, removing tissue debris, and tissue remodeling. One of the key mediators of these metabolic changes is the transcription factor hypoxia-inducible factor 1α (HIF-1α). Single-cell dynamics have been shown to be an important determinant of cell behavior; however, despite the importance of HIF-1α, little is known about its single-cell dynamics or their effect on metabolism. To address this knowledge gap, here we optimized a HIF-1α fluorescent reporter and applied it to study single-cell dynamics. First, we showed that single cells are likely able to differentiate multiple levels of prolyl hydroxylase inhibition, a marker of metabolic change, via HIF-1α activity. We then applied a physiological stimulus known to trigger metabolic change, interferon-γ, and observed heterogeneous, oscillatory HIF-1α responses in single cells. Finally, we input these dynamics into a mathematical model of HIF-1α-regulated metabolism and discovered a profound difference between cells exhibiting high versus low HIF-1α activation. Specifically, we found cells with high HIF-1α activation are able to meaningfully reduce flux through the tricarboxylic acid cycle and show a notable increase in the NAD+/NADH ratio compared with cells displaying low HIF-1α activation. Altogether, this work demonstrates an optimized reporter for studying HIF-1α in single cells and reveals previously unknown principles of HIF-1α activation.
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Affiliation(s)
- Stevan Jeknić
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Takamasa Kudo
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA
| | - Joanna J Song
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, California, USA.
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14
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Yfantis A, Mylonis I, Chachami G, Nikolaidis M, Amoutzias GD, Paraskeva E, Simos G. Transcriptional Response to Hypoxia: The Role of HIF-1-Associated Co-Regulators. Cells 2023; 12:cells12050798. [PMID: 36899934 PMCID: PMC10001186 DOI: 10.3390/cells12050798] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/22/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
The Hypoxia Inducible Factor 1 (HIF-1) plays a major role in the cellular response to hypoxia by regulating the expression of many genes involved in adaptive processes that allow cell survival under low oxygen conditions. Adaptation to the hypoxic tumor micro-environment is also critical for cancer cell proliferation and therefore HIF-1 is also considered a valid therapeutical target. Despite the huge progress in understanding regulation of HIF-1 expression and activity by oxygen levels or oncogenic pathways, the way HIF-1 interacts with chromatin and the transcriptional machinery in order to activate its target genes is still a matter of intense investigation. Recent studies have identified several different HIF-1- and chromatin-associated co-regulators that play important roles in the general transcriptional activity of HIF-1, independent of its expression levels, as well as in the selection of binding sites, promoters and target genes, which, however, often depends on cellular context. We review here these co-regulators and examine their effect on the expression of a compilation of well-characterized HIF-1 direct target genes in order to assess the range of their involvement in the transcriptional response to hypoxia. Delineating the mode and the significance of the interaction between HIF-1 and its associated co-regulators may offer new attractive and specific targets for anticancer therapy.
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Affiliation(s)
- Angelos Yfantis
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, BIOPOLIS, 41500 Larissa, Greece; (A.Y.); (I.M.); (G.C.)
| | - Ilias Mylonis
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, BIOPOLIS, 41500 Larissa, Greece; (A.Y.); (I.M.); (G.C.)
| | - Georgia Chachami
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, BIOPOLIS, 41500 Larissa, Greece; (A.Y.); (I.M.); (G.C.)
| | - Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, BIOPOLIS, 41500 Larissa, Greece; (M.N.); (G.D.A.)
| | - Grigorios D. Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, BIOPOLIS, 41500 Larissa, Greece; (M.N.); (G.D.A.)
| | - Efrosyni Paraskeva
- Laboratory of Physiology, Faculty of Medicine, University of Thessaly, BIOPOLIS, 41500 Larissa, Greece;
| | - George Simos
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, BIOPOLIS, 41500 Larissa, Greece; (A.Y.); (I.M.); (G.C.)
- Gerald Bronfman Department of Oncology, Faculty of Medicine, McGill University, Montreal, QC H4A 3T2, Canada
- Correspondence:
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15
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Subramani A, Hite MEL, Garcia S, Maxwell J, Kondee H, Millican GE, McClelland EE, Seipelt-Thiemann RL, Nelson DE. Regulation of macrophage IFNγ-stimulated gene expression by the transcriptional coregulator CITED1. J Cell Sci 2023; 136:jcs260529. [PMID: 36594555 PMCID: PMC10112972 DOI: 10.1242/jcs.260529] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/21/2022] [Indexed: 01/04/2023] Open
Abstract
Macrophages serve as a first line of defense against microbial pathogens. Exposure to interferon-γ (IFNγ) increases interferon-stimulated gene (ISG) expression in these cells, resulting in enhanced antimicrobial and proinflammatory activity. Although this response must be sufficiently vigorous to ensure the successful clearance of pathogens, it must also be carefully regulated to prevent tissue damage. This is controlled in part by CBP/p300-interacting transactivator with glutamic acid/aspartic acid-rich carboxyl-terminal domain 2 (CITED2), a transcriptional coregulator that limits ISG expression by inhibiting STAT1 and IRF1. Here, we show that the closely related Cited1 is an ISG, which is expressed in a STAT1-dependent manner, and that IFNγ stimulates the nuclear accumulation of CITED1 protein. In contrast to CITED2, ectopic CITED1 enhanced the expression of a subset of ISGs, including Ccl2, Ifit3b, Isg15 and Oas2. This effect was reversed in a Cited1-null cell line produced by CRISPR-based genomic editing. Collectively, these data show that CITED1 maintains proinflammatory gene expression during periods of prolonged IFNγ exposure and suggest that there is an antagonistic relationship between CITED proteins in the regulation of macrophage inflammatory function. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Aarthi Subramani
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Maria E. L. Hite
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Sarah Garcia
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Jack Maxwell
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Hursha Kondee
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Grace E. Millican
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Erin E. McClelland
- College of Osteopathic Medicine, Marian University, Indianapolis, IN 46222, USA
| | | | - David E. Nelson
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA
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16
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Wen B, Zhang W, Zhang Y, Lei H, Cao Y, Li W, Wang W. Self-Effected Allosteric Coupling and Cooperativity in Hypoxic Response Regulation with Disordered Proteins. J Phys Chem Lett 2022; 13:9201-9209. [PMID: 36170455 DOI: 10.1021/acs.jpclett.2c02065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Hypersensitive regulation of cellular hypoxic response relies on cooperative displacement of one disordered protein (HIF-1α) by another disordered protein (CITED2) from the target in a negative feedback loop. Considering the weak intramolecule coupling in disordered proteins, the molecular mechanism of high cooperativity in the molecular displacement event remains elusive. Herein, we show that disordered proteins utilize a "self-effected allostery" mechanism to achieve high binding cooperativity. Different from the conventional allostery mechanisms shown by many structured or disordered proteins, this mechanism utilizes one part of the disordered protein as the effector to trigger the allosteric coupling and enhance the binding of the remaining part of the same disordered protein, contributing to high cooperativity of the displacement event. The conserved charge motif of CITED2 is the key determinant of the molecular displacement event by serving as the effector of allosteric coupling. Such self-effected allostery provides an efficient strategy to achieve high cooperativity in the molecular events involving disordered proteins.
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Affiliation(s)
- Bin Wen
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Weiwei Zhang
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Yangyang Zhang
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Hai Lei
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Yi Cao
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wenfei Li
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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17
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Lu M, Liu Y, Xian Z, Yu X, Chen J, Tan S, Zhang P, Guo Y. VEGF to CITED2 ratio predicts the collateral circulation of acute ischemic stroke. Front Neurol 2022; 13:1000992. [PMID: 36247751 PMCID: PMC9563238 DOI: 10.3389/fneur.2022.1000992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022] Open
Abstract
Objective The research objective was to evaluate the predicting role of the vascular endothelial growth factor to CBP/P300-interacting transactivator with Glu/Asp-rich C-terminal domain 2 Ratio (VEGF/CITED2) from peripheral blood mononuclear cells (PBMCs) in the collateral circulation of acute ischemic stroke (AIS). Methods In an observational study of patients with AIS, the western blot was applied to test the protein expression of VEGF and CITED2. Then, we calculated the VEGF/CITED2 and collected other clinical data. Binary logistic regression analysis between collateral circulation and clinical data was performed. Finally, receiver operating characteristic (ROC) curve analysis was used to explore the predictive value of VEGF/CITED2. Results A total of 67 patients with AIS were included in the study. Binary logistic regression analysis indicated the VEGF/CITED2 (OR 165.79, 95%CI 7.25–3,791.54, P = 0.001) was an independent protective factor. The ROC analyses showed an area under the ROC curve of the VEGF/CITED2 was 0.861 (95%CI 0.761–0.961). The optimal cutoff value of 1.013 for VEGF/CITED2 had a sensitivity of 89.1% and a specificity of 85.7%. Conclusion In patients with AIS, the VEGF/CITED2 was related to the establishment of collateral circulation. The VEGF/CITED2 is a potentially valuable biomarker for predicting collateral circulation. Clinical trial registration ClinicalTrials.gov, identifier: NCT05345366.
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Affiliation(s)
- Minyi Lu
- Department of Neurology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yuben Liu
- Department of Neurology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zhiqiang Xian
- Department of Neurology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoyao Yu
- Department of Neurology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Chen
- Department of Neurology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Sheng Tan
- Department of Neurology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Peidong Zhang
- Department of Cardiology, Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Peidong Zhang
| | - Yang Guo
- Department of Neurology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Yang Guo
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18
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Yang L, Yang G, Bing Z, Tian Y, Huang L, Niu Y, Yang L. Accelerating the discovery of anticancer peptides targeting lung and breast cancers with the Wasserstein autoencoder model and PSO algorithm. Brief Bioinform 2022; 23:6658854. [PMID: 35945135 DOI: 10.1093/bib/bbac320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/14/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
In the development of targeted drugs, anticancer peptides (ACPs) have attracted great attention because of their high selectivity, low toxicity and minimal non-specificity. In this work, we report a framework of ACPs generation, which combines Wasserstein autoencoder (WAE) generative model and Particle Swarm Optimization (PSO) forward search algorithm guided by attribute predictive model to generate ACPs with desired properties. It is well known that generative models based on Variational AutoEncoder (VAE) and Generative Adversarial Networks (GAN) are difficult to be used for de novo design due to the problems of posterior collapse and difficult convergence of training. Our WAE-based generative model trains more successfully (lower perplexity and reconstruction loss) than both VAE and GAN-based generative models, and the semantic connections in the latent space of WAE accelerate the process of forward controlled generation of PSO, while VAE fails to capture this feature. Finally, we validated our pipeline on breast cancer targets (HIF-1) and lung cancer targets (VEGR, ErbB2), respectively. By peptide-protein docking, we found candidate compounds with the same binding sites as the peptides carried in the crystal structure but with higher binding affinity and novel structures, which may be potent antagonists that interfere with these target-mediated signaling.
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Affiliation(s)
- Lijuan Yang
- Institute of modern physics, Chinese Academy of Science, Lanzhou 730000, China.,School of Physics and Technology, Lanzhou University, Lanzhou 730000, China.,School of Physics, University of Chinese Academy of Science, Beijing 100049, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516000, China
| | - Guanghui Yang
- Institute of modern physics, Chinese Academy of Science, Lanzhou 730000, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516000, China
| | - Zhitong Bing
- Institute of modern physics, Chinese Academy of Science, Lanzhou 730000, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516000, China
| | - Yuan Tian
- Institute of modern physics, Chinese Academy of Science, Lanzhou 730000, China.,School of Information Science and Engineering, Lanzhou University, Lanzhou 730000, China
| | - Liang Huang
- School of Physics and Technology, Lanzhou University, Lanzhou 730000, China
| | - Yuzhen Niu
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo 255000, China
| | - Lei Yang
- Institute of modern physics, Chinese Academy of Science, Lanzhou 730000, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516000, China
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19
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Sawant M, Mahajan K, Renganathan A, Weimholt C, Luo J, Kukshal V, Jez JM, Jeon MS, Zhang B, Li T, Fang B, Luo Y, Lawrence NJ, Lawrence HR, Feng FY, Mahajan NP. Chronologically modified androgen receptor in recurrent castration-resistant prostate cancer and its therapeutic targeting. Sci Transl Med 2022; 14:eabg4132. [PMID: 35704598 PMCID: PMC10259236 DOI: 10.1126/scitranslmed.abg4132] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Resistance to second-generation androgen receptor (AR) antagonists such as enzalutamide is an inevitable consequence in patients with castration-resistant prostate cancer (CRPC). There are no effective therapeutic options for this recurrent disease. The expression of truncated AR variant 7 (AR-V7) has been suggested to be one mechanism of resistance; however, its low frequency in patients with CRPC does not explain the almost universal acquisition of resistance. We noted that the ability of AR to translocate to nucleus in an enzalutamide-rich environment opens up the possibility of a posttranslational modification in AR that is refractory to enzalutamide binding. Chemical proteomics in enzalutamide-resistant CRPC cells revealed acetylation at Lys609 in the zinc finger DNA binding domain of AR (acK609-AR) that not only allowed AR translocation but also galvanized a distinct global transcription program, conferring enzalutamide insensitivity. Mechanistically, acK609-AR was recruited to the AR and ACK1/TNK2 enhancers, up-regulating their transcription. ACK1 kinase-mediated AR Y267 phosphorylation was a prerequisite for AR K609 acetylation, which spawned positive feedback loops at both the transcriptional and posttranslational level that regenerated and sustained high AR and ACK1 expression. Consistent with these findings, oral and subcutaneous treatment with ACK1 small-molecule inhibitor, (R)-9b, not only curbed AR Y267 phosphorylation and subsequent K609 acetylation but also compromised enzalutamide-resistant CRPC xenograft tumor growth in mice. Overall, these data uncover chronological modification events in AR that allows prostate cancer to evolve through progressive stages to reach the resilient recurrent CRPC stage, opening up a therapeutic vulnerability.
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Affiliation(s)
- Mithila Sawant
- Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Kiran Mahajan
- Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO 63110, USA
| | - Arun Renganathan
- Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Cody Weimholt
- Department of Anatomic and Clinical Pathology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Jingqin Luo
- Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO 63110, USA
| | - Vandna Kukshal
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63110, USA
| | - Joseph M. Jez
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63110, USA
| | - Myung Sik Jeon
- Siteman Cancer Center, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO 63110, USA
| | - Bo Zhang
- Bioinformatics Research Core, Center of Regenerative Medicine, Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Tiandao Li
- Bioinformatics Research Core, Center of Regenerative Medicine, Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Bin Fang
- Drug Discovery Department, Moffitt Cancer Center, Department of Oncologic Sciences, University of South Florida, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
| | - Yunting Luo
- Drug Discovery Department, Moffitt Cancer Center, Department of Oncologic Sciences, University of South Florida, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
| | - Nicholas J. Lawrence
- Drug Discovery Department, Moffitt Cancer Center, Department of Oncologic Sciences, University of South Florida, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
| | - Harshani R. Lawrence
- Drug Discovery Department, Moffitt Cancer Center, Department of Oncologic Sciences, University of South Florida, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
| | - Felix Y. Feng
- Helen Diller Family Cancer Research Building, 1450 Third Street, Room 383, University of California, San Francisco, CA 94158, USA
| | - Nupam P. Mahajan
- Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO 63110, USA
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20
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Staller MV, Ramirez E, Kotha SR, Holehouse AS, Pappu RV, Cohen BA. Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains. Cell Syst 2022; 13:334-345.e5. [PMID: 35120642 PMCID: PMC9241528 DOI: 10.1016/j.cels.2022.01.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 10/20/2021] [Accepted: 01/05/2022] [Indexed: 01/01/2023]
Abstract
Acidic activation domains are intrinsically disordered regions of the transcription factors that bind coactivators. The intrinsic disorder and low evolutionary conservation of activation domains have made it difficult to identify the sequence features that control activity. To address this problem, we designed thousands of variants in seven acidic activation domains and measured their activities with a high-throughput assay in human cell culture. We found that strong activation domain activity requires a balance between the number of acidic residues and aromatic and leucine residues. These findings motivated a predictor of acidic activation domains that scans the human proteome for clusters of aromatic and leucine residues embedded in regions of high acidity. This predictor identifies known activation domains and accurately predicts previously unidentified ones. Our results support a flexible acidic exposure model of activation domains in which the acidic residues solubilize hydrophobic motifs so that they can interact with coactivators. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Max V Staller
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA; Center for Computational Biology, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Eddie Ramirez
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA
| | - Sanjana R Kotha
- Center for Computational Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA; Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Rohit V Pappu
- Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Barak A Cohen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA.
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21
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Multivalency enables unidirectional switch-like competition between intrinsically disordered proteins. Proc Natl Acad Sci U S A 2022; 119:2117338119. [PMID: 35012986 PMCID: PMC8784115 DOI: 10.1073/pnas.2117338119] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 12/31/2022] Open
Abstract
Intrinsically disordered proteins must compete for binding to common regulatory targets to carry out their biological functions. Previously, we showed that the activation domains of two disordered proteins, the transcription factor HIF-1α and its negative regulator CITED2, function as a unidirectional, allosteric molecular switch to control transcription of critical adaptive genes under conditions of oxygen deprivation. These proteins achieve transcriptional control by competing for binding to the TAZ1 domain of the transcriptional coactivators CREB-binding protein (CBP) and p300 (CREB: cyclic-AMP response element binding protein). To characterize the mechanistic details behind this molecular switch, we used solution NMR spectroscopy and complementary biophysical methods to determine the contributions of individual binding motifs in CITED2 to the overall competition process. An N-terminal region of the CITED2 activation domain, which forms a helix when bound to TAZ1, plays a critical role in initiating competition with HIF-1α by enabling formation of a ternary complex in a process that is highly dependent on the dynamics and disorder of the competing partners. Two other conserved binding motifs in CITED2, the LPEL motif and an aromatic/hydrophobic motif that we term ϕC, function synergistically to enhance binding of CITED2 and inhibit rebinding of HIF-1α. The apparent unidirectionality of competition between HIF-1α and CITED2 is lost when one or more of these binding regions is altered by truncation or mutation of the CITED2 peptide. Our findings illustrate the complexity of molecular interactions involving disordered proteins containing multivalent interaction motifs and provide insight into the unique mechanisms by which disordered proteins compete for occupancy of common molecular targets within the cell.
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22
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Hóbor F, Hegedüs Z, Ibarra AA, Petrovicz VL, Bartlett GJ, Sessions RB, Wilson AJ, Edwards TA. Understanding p300-transcription factor interactions using sequence variation and hybridization. RSC Chem Biol 2022; 3:592-603. [PMID: 35656479 PMCID: PMC9092470 DOI: 10.1039/d2cb00026a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/10/2022] [Indexed: 11/21/2022] Open
Abstract
The hypoxic response is central to cell function and plays a significant role in the growth and survival of solid tumours. HIF-1 regulates the hypoxic response by activating over 100...
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Affiliation(s)
- Fruzsina Hóbor
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Zsófia Hegedüs
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H-6720 Szeged Hungary
| | - Amaurys Avila Ibarra
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Vencel L Petrovicz
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H-6720 Szeged Hungary
| | - Gail J Bartlett
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
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23
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Chu WT, Yan Z, Chu X, Zheng X, Liu Z, Xu L, Zhang K, Wang J. Physics of biomolecular recognition and conformational dynamics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2021; 84:126601. [PMID: 34753115 DOI: 10.1088/1361-6633/ac3800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Biomolecular recognition usually leads to the formation of binding complexes, often accompanied by large-scale conformational changes. This process is fundamental to biological functions at the molecular and cellular levels. Uncovering the physical mechanisms of biomolecular recognition and quantifying the key biomolecular interactions are vital to understand these functions. The recently developed energy landscape theory has been successful in quantifying recognition processes and revealing the underlying mechanisms. Recent studies have shown that in addition to affinity, specificity is also crucial for biomolecular recognition. The proposed physical concept of intrinsic specificity based on the underlying energy landscape theory provides a practical way to quantify the specificity. Optimization of affinity and specificity can be adopted as a principle to guide the evolution and design of molecular recognition. This approach can also be used in practice for drug discovery using multidimensional screening to identify lead compounds. The energy landscape topography of molecular recognition is important for revealing the underlying flexible binding or binding-folding mechanisms. In this review, we first introduce the energy landscape theory for molecular recognition and then address four critical issues related to biomolecular recognition and conformational dynamics: (1) specificity quantification of molecular recognition; (2) evolution and design in molecular recognition; (3) flexible molecular recognition; (4) chromosome structural dynamics. The results described here and the discussions of the insights gained from the energy landscape topography can provide valuable guidance for further computational and experimental investigations of biomolecular recognition and conformational dynamics.
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Affiliation(s)
- Wen-Ting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Zhiqiang Yan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Xiakun Chu
- Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, NY 11794, United States of America
| | - Xiliang Zheng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Zuojia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Li Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Kun Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Jin Wang
- Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, NY 11794, United States of America
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24
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Appling FD, Berlow RB, Stanfield RL, Dyson HJ, Wright PE. The molecular basis of allostery in a facilitated dissociation process. Structure 2021; 29:1327-1338.e5. [PMID: 34520739 PMCID: PMC8642270 DOI: 10.1016/j.str.2021.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/22/2021] [Accepted: 07/21/2021] [Indexed: 12/29/2022]
Abstract
Facilitated dissociation provides a mechanism by which high-affinity complexes can be rapidly disassembled. The negative feedback regulator CITED2 efficiently downregulates the hypoxic response by displacing the hypoxia-inducible transcription factor HIF-1α from the TAZ1 domain of the transcriptional coactivators CREB-binding protein (CBP) and p300. Displacement occurs by a facilitated dissociation mechanism involving a transient ternary intermediate formed by binding of the intrinsically disordered CITED2 activation domain to the TAZ1:HIF-1α complex. The short lifetime of the intermediate precludes straightforward structural investigations. To obtain insights into the molecular determinants of facilitated dissociation, we model the ternary intermediate by generating a fusion peptide composed of the primary CITED2 and HIF-1α binding motifs. X-ray crystallographic and NMR studies of the fusion peptide complex reveal TAZ1-mediated negative cooperativity that results in nearly mutually exclusive binding of specific CITED2 and HIF-1α interaction motifs, providing molecular-level insights into the allosteric switch that terminates the hypoxic response.
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Affiliation(s)
- Francis D Appling
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Rebecca B Berlow
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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25
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Qin X, Chen H, Tu L, Ma Y, Liu N, Zhang H, Li D, Riedl B, Bierer D, Yin F, Li Z. Potent Inhibition of HIF1α and p300 Interaction by a Constrained Peptide Derived from CITED2. J Med Chem 2021; 64:13693-13703. [PMID: 34472840 DOI: 10.1021/acs.jmedchem.1c01043] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Disrupting the interaction between HIF1α and p300 is a promising strategy to modulate the hypoxia response of tumor cells. Herein, we designed a constrained peptide inhibitor derived from the CITED2/p300 complex to disturb the HIF1α/p300 interaction. Through truncation/mutation screening and a terminal aspartic acid-stabilized strategy, a constrained peptide was constructed with outstanding biochemical/biophysical properties, especially in binding affinity, cell penetration, and serum stability. To date, our study was the first one to showcase that stabilized peptides derived from CITED2 using helix-stabilizing methods acted as a promising candidate for modulating hypoxia-inducible signaling.
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Affiliation(s)
- Xuan Qin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Hailing Chen
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Licheng Tu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yue Ma
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Na Liu
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Haowei Zhang
- Key Lab in Healthy Science and Technology, Division of Life Science, Shenzhen Graduate School of Tsinghua University, Shenzhen 518055, China
| | - Di Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Bernd Riedl
- Department of Medicinal Chemistry, Bayer AG, Aprather Weg 18A, Wuppertal 42096, Germany
| | - Donald Bierer
- Department of Medicinal Chemistry, Bayer AG, Aprather Weg 18A, Wuppertal 42096, Germany
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.,Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518055, China
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26
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Weinhouse C. The roles of inducible chromatin and transcriptional memory in cellular defense system responses to redox-active pollutants. Free Radic Biol Med 2021; 170:85-108. [PMID: 33789123 PMCID: PMC8382302 DOI: 10.1016/j.freeradbiomed.2021.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/17/2022]
Abstract
People are exposed to wide range of redox-active environmental pollutants. Air pollution, heavy metals, pesticides, and endocrine disrupting chemicals can disrupt cellular redox status. Redox-active pollutants in our environment all trigger their own sets of specific cellular responses, but they also activate a common set of general stress responses that buffer the cell against homeostatic insults. These cellular defense system (CDS) pathways include the heat shock response, the oxidative stress response, the hypoxia response, the unfolded protein response, the DNA damage response, and the general stress response mediated by the stress-activated p38 mitogen-activated protein kinase. Over the past two decades, the field of environmental epigenetics has investigated epigenetic responses to environmental pollutants, including redox-active pollutants. Studies of these responses highlight the role of chromatin modifications in controlling the transcriptional response to pollutants and the role of transcriptional memory, often referred to as "epigenetic reprogramming", in predisposing previously exposed individuals to more potent transcriptional responses on secondary challenge. My central thesis in this review is that high dose or chronic exposure to redox-active pollutants leads to transcriptional memories at CDS target genes that influence the cell's ability to mount protective responses. To support this thesis, I will: (1) summarize the known chromatin features required for inducible gene activation; (2) review the known forms of transcriptional memory; (3) discuss the roles of inducible chromatin and transcriptional memory in CDS responses that are activated by redox-active environmental pollutants; and (4) propose a conceptual framework for CDS pathway responsiveness as a readout of total cellular exposure to redox-active pollutants.
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Affiliation(s)
- Caren Weinhouse
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, 97214, USA.
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27
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Mezera MA, Li W, Liu L, Meidan R, Peñagaricano F, Wiltbank MC. Effect of natural pre-luteolytic prostaglandin F2α pulses on the bovine luteal transcriptome during spontaneous luteal regression. Biol Reprod 2021; 105:1016-1029. [PMID: 34170313 DOI: 10.1093/biolre/ioab123] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 06/03/2021] [Accepted: 06/20/2021] [Indexed: 01/14/2023] Open
Abstract
The pulsatile pattern of prostaglandin F2alpha (PGF) secretion during spontaneous luteolysis is well-documented, with multiple pulses of exogenous PGF necessary to induce regression using physiologic concentrations of PGF. However, during spontaneous regression, the earliest pulses of PGF are small and not associated with detectable changes in circulating progesterone (P4), bringing into question what, if any, role these early, subluteolytic PGF pulses have during physiologic regression. To investigate the effect of small PGF pulses, luteal biopsies were collected throughout natural luteolysis in conjunction with bihourly blood samples to determine circulating P4 and PGF metabolite to retrospectively assign biopsies to early and later regression. Whole transcriptome analysis was conducted on CL biopsies. Early PGF pulses altered the luteal transcriptome, inducing differential expression of 210 genes (Q < 0.05) during early regression, compared to 4615 differentially expressed genes during later regression. In early regression, few of these differentially expressed genes were directly associated with luteolysis, rather there were changes in local steroid and glutathione metabolism. Most (94%) differentially expressed genes from early regression were also differentially expressed during later regression, with 98% of these continuing to be altered in the same direction compared to CL at a similar stage of the cycle that had not yet been exposed to PGF. Thus, early, subluteolytic PGF pulses impact the luteal transcriptome, though not by altering steroidogenesis or causing direct inhibition of cellular function. Rather, small pulses alter pathways resulting in removal of cellular support systems, which may sensitize the CL to later pulses of PGF.
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Affiliation(s)
- Megan A Mezera
- Department of Animal & Dairy Sciences and 2Endocrinology and Reproductive Physiology Program, University of Wisconsin-Madison, Madison, WI 53706, USA.,USDA Dairy Forage Research Center, Madison, WI 53706, USA
| | - Wenli Li
- USDA Dairy Forage Research Center, Madison, WI 53706, USA
| | - Lihe Liu
- Department of Animal & Dairy Sciences and 2Endocrinology and Reproductive Physiology Program, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Rina Meidan
- Department of Animal Sciences, The Hebrew University of Jerusalem
| | - Francisco Peñagaricano
- Department of Animal & Dairy Sciences and 2Endocrinology and Reproductive Physiology Program, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Milo C Wiltbank
- Department of Animal & Dairy Sciences and 2Endocrinology and Reproductive Physiology Program, University of Wisconsin-Madison, Madison, WI 53706, USA
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28
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Shalmani A, Ullah U, Muhammad I, Zhang D, Sharif R, Jia P, Saleem N, Gul N, Rakhmanova A, Tahir MM, Chen KM, An N. The TAZ domain-containing proteins play important role in the heavy metals stress biology in plants. ENVIRONMENTAL RESEARCH 2021; 197:111030. [PMID: 33774015 DOI: 10.1016/j.envres.2021.111030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/11/2021] [Accepted: 03/13/2021] [Indexed: 06/12/2023]
Abstract
TAZ (transcriptional coactivator with PDZ-binding) zinc finger domains, also known as transcription adaptor putative zinc finger domains, that control diverse function in plant growth and development. Here, in the present study, we evaluated the role of the TAZ domain-containing gene in response to various heavy metals. Initially, we found a total of 3, 7, 8, 9, 9, 9, 7, 14, 6, 10, and 6 proteins containing TAZ domain in stiff brome, millet, sorghum, potato, pepper, maize, rice, apple, peach, pear, and tomato genome that could trigger the plant resistance against various heavy metals, respectively. Various in-silico approaches were applied such as duplication, phylogenetic analysis, and gene structure, to understand the basic features of the TAZ domain-containing genes in plants. Gene expression analyses were also performed under heavy metals (Cr, Zn, Ni, Cd, Co, Fe, Mn, and Pb). The results of quantitative real-time PCR analysis indicated that the TAZ gene family members were differentially expressed under different heavy metals. We further characterized the functions of the TAZ domain-containing gene under the heavy metal stresses by overexpressing the OsTAZ4 gene in Arabidopsis. The TAZ genes could promote plant resistance against various heavy metals by interacting with OsMYB34 and OsFHA9 transcription factors. The results will contribute to elucidate the relationship of TAZ proteins with heavy metals stresses and also ascertain the biological function in plant growth and development.
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Affiliation(s)
- Abdullah Shalmani
- College of Horticulture, Northwest A and F University, Yangling, Shaanxi Province, 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Uzair Ullah
- Department of Genetics, Hazara University, Manshera, KPK, Pakistan.
| | - Izhar Muhammad
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi Province, 712100, China; College of Agronomy, Northwest A and F University, Yangling, Shaanxi Province, 712100, China.
| | - Dong Zhang
- College of Horticulture, Northwest A and F University, Yangling, Shaanxi Province, 712100, China.
| | - Rahat Sharif
- Department of Horticulture, School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, PR China.
| | - Peng Jia
- College of Horticulture, Northwest A and F University, Yangling, Shaanxi Province, 712100, China.
| | - Noor Saleem
- College of Agronomy, Northwest A and F University, Yangling, Shaanxi Province, 712100, China.
| | - Nazish Gul
- Department of Genetics, Hazara University, Manshera, KPK, Pakistan.
| | - Aizhan Rakhmanova
- College of Food Science and Engineering, Northwest A & F University, Yangling, Shaanxi Province, 712100, China.
| | - Muhammad Mobeen Tahir
- College of Horticulture, Northwest A and F University, Yangling, Shaanxi Province, 712100, China.
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Na An
- College of Horticulture, Northwest A and F University, Yangling, Shaanxi Province, 712100, China; College of Life Sciences, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
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A gain-of-function mutation in CITED2 is associated with congenital heart disease. Mutat Res 2021; 822:111741. [PMID: 33706167 DOI: 10.1016/j.mrfmmm.2021.111741] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/26/2021] [Indexed: 12/20/2022]
Abstract
CITED2 is a transcription co-activator that interacts with TFAP2 and CBP/ P300 transcription factors to regulate the proliferation and differentiation of the cardiac progenitor cells. It acts upstream to NODAL-PITX2 pathways and regulates the left-right asymmetry. Both human genetic and model organism studies have shown that altered expression of CITED2 causes various forms of congenital heart disease. Therefore, we sought to screen the coding region of CITED2 to identify rare genetic variants and assess their impact on the structure and function of the protein. Here, we have screened 271 non-syndromic, sporadic CHD cases by Sanger's sequencing method and detected a non-synonymous variant (c.301C>T, p.P101S) and two synonymous variants (c.21C>A, p.A7A; c.627C>G, p.P209P). The non-synonymous variant c.301C>T (rs201639244) is a rare variant with a minor allele frequency of 0.00011 in the gnomAD browser and 0.0018 in the present study. in vitro analysis has demonstrated that p.P101S mutation upregulates the expression of downstream target genes Gata4, Mef2c, Nfatc1&2, Nodal, Pitx2, and Tbx5 in P19 cells. Luciferase reporter assay also demonstrates enhanced activation of downstream target promoters. Further, in silico analyses implicate that increased activity of mutant CITED2 is possibly due to phosphorylation of Serine residue by proline-directed kinases. Homology modeling and alignment analysis have also depicted differences in hydrogen bonding and tertiary structures of wild-type versus mutant protein. The impact of synonymous variations on the mRNA structure of CITED2has been analyzed by Mfold and relative codon bias calculations. Mfold results have revealed that both the synonymous variants can alter the mRNA structure and stability. Relative codon usage analysis has suggested that the rate of translation is attenuated due to these variations. Altogether, our results from genetic screening as well as in vitro and in silico studies support a possible role of nonsynonymous and synonymous mutations in CITED2contributing to pathogenesis of CHD.
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30
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Baddar NWAH, Dwaraka VB, Ponomareva LV, Thorson JS, Voss SR. Chemical genetics of regeneration: Contrasting temporal effects of CoCl
2
on axolotl tail regeneration. Dev Dyn 2021; 250:852-865. [DOI: 10.1002/dvdy.294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/19/2020] [Indexed: 12/16/2022] Open
Affiliation(s)
- Nour W. Al Haj Baddar
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center University of Kentucky Lexington Kentucky USA
| | - Varun B. Dwaraka
- Department of Biology University of Kentucky Lexington Kentucky USA
| | - Larissa V. Ponomareva
- College of Pharmacy and Center for Pharmaceutical Research and Innovation University of Kentucky Lexington Kentucky USA
| | - Jon S. Thorson
- College of Pharmacy and Center for Pharmaceutical Research and Innovation University of Kentucky Lexington Kentucky USA
| | - S. Randal Voss
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center University of Kentucky Lexington Kentucky USA
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Zhang Q, Han Z, Zhu Y, Chen J, Li W. Role of hypoxia inducible factor-1 in cancer stem cells (Review). Mol Med Rep 2020; 23:17. [PMID: 33179080 PMCID: PMC7673349 DOI: 10.3892/mmr.2020.11655] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/25/2020] [Indexed: 02/06/2023] Open
Abstract
Cancer stem cells (CSCs) have been found to play a decisive role in cancer recurrence, metastasis, and chemo‑, radio‑ and immuno‑resistance. Understanding the mechanism of CSC self‑renewal and proliferation may help overcome the limitations of clinical treatment. The microenvironment of tumor growth consists of a lack of oxygen, and hypoxia has been confirmed to induce cancer cell invasion, metastasis and epithelial‑mesenchymal transition, and is usually associated with poor prognosis and low survival rates. Hypoxia inducible factor‑1 (HIF‑1) can be stably expressed under hypoxia and act as an important molecule to regulate the development of CSCs, but the specific mechanism remains unclear. The present review attempted to explain the role of HIF‑1 in the generation and maintenance of CSCs from the perspective of epigenetics, metabolic reprogramming, tumor immunity, CSC markers, non‑coding RNA and signaling pathways associated with HIF‑1, in order to provide novel targets with HIF‑1 as the core for clinical treatment, and extend the life of patients.
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Affiliation(s)
- Qi Zhang
- Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China
| | - Zhenzhen Han
- Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China
| | - Yanbo Zhu
- Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China
| | - Jingcheng Chen
- Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China
| | - Wei Li
- Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China
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Helle E, Ampuja M, Antola L, Kivelä R. Flow-Induced Transcriptomic Remodeling of Endothelial Cells Derived From Human Induced Pluripotent Stem Cells. Front Physiol 2020; 11:591450. [PMID: 33178051 PMCID: PMC7593792 DOI: 10.3389/fphys.2020.591450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/16/2020] [Indexed: 12/31/2022] Open
Abstract
The vascular system is essential for the development and function of all organs and tissues in our body. The molecular signature and phenotype of endothelial cells (EC) are greatly affected by blood flow-induced shear stress, which is a vital component of vascular development and homeostasis. Recent advances in differentiation of ECs from human induced pluripotent stem cells (hiPSC) have enabled development of in vitro experimental models of the vasculature containing cells from healthy individuals or from patients harboring genetic variants or diseases of interest. Here we have used hiPSC-derived ECs and bulk- and single-cell RNA sequencing to study the effect of flow on the transcriptomic landscape of hiPSC-ECs and their heterogeneity. We demonstrate that hiPS-ECs are plastic and they adapt to flow by expressing known flow-induced genes. Single-cell RNA sequencing showed that flow induced a more homogenous and homeostatically more stable EC population compared to static cultures, as genes related to cell polarization, barrier formation and glucose and fatty acid transport were induced. The hiPS-ECs increased both arterial and venous markers when exposed to flow. Interestingly, while in general there was a greater increase in the venous markers, one cluster with more arterial-like hiPS-ECs was detected. Single-cell RNA sequencing revealed that not all hiPS-ECs are similar even after sorting, but exposing them to flow increases their homogeneity. Since hiPS-ECs resemble immature ECs and demonstrate high plasticity in response to flow, they provide an excellent model to study vascular development.
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Affiliation(s)
- Emmi Helle
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- New Children’s Hospital, and Pediatric Research Center Helsinki University Hospital, Helsinki, Finland
| | - Minna Ampuja
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Laura Antola
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Riikka Kivelä
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Wihuri Research Institute, Helsinki, Finland
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33
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Abstract
Cbp/P300 interacting transactivator with Glu/Asp-rich carboxy-terminal domain 2 (CITED2) is a transcription co-factor that interacts with several other transcription factors and co-factors, and serves critical roles in fundamental cell processes, including proliferation, apoptosis, differentiation, migration and autophagy. The interacting transcription factors or co-factors of CITED2 include LIM homeobox 2, transcription factor AP-2, SMAD2/3, peroxisome proliferator-activated receptor γ, oestrogen receptor, MYC, Nucleolin and p300/CBP, which regulate downstream gene expression, and serve important roles in the aforementioned fundamental cell processes. Emerging evidence has demonstrated that CITED2 serves an essential role in embryonic and adult tissue stem cells, including hematopoietic stem cells and tendon-derived stem/progenitor cells. Additionally, CITED2 has been reported to function in different types of cancer. Although the functions of CITED2 in different tissues vary depending on the interaction partner, altered CITED2 expression or altered interactions with transcription factors or co-factors result in alterations of fundamental cell processes, and may affect stem cell maintenance or cancer cell survival. The aim of this review is to summarize the molecular mechanisms of CITED2 function and how it serves a role in stem cells and different types of cancer based on the currently available literature.
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Abstract
The oxygen levels organ and tissue microenvironments vary depending on the distance of their vasculature from the left ventricle of the heart. For instance, the oxygen levels of lymph nodes and the spleen are significantly lower than that in atmospheric air. Cellular detection of oxygen and their response to low oxygen levels can exert a significant impact on virus infection. Generally, viruses that naturally infect well-oxygenated organs are less able to infect cells under hypoxic conditions. Conversely, viruses that infect organs under lower oxygen tensions thrive under hypoxic conditions. This suggests that in vitro experiments performed exclusively under atmospheric conditions ignores oxygen-induced modifications in both host and viral responses. Here, we review the mechanisms of how cells adapt to low oxygen tensions and its impact on viral infections. With growing evidence supporting the role of oxygen microenvironments in viral infections, this review highlights the importance of factoring oxygen concentrations into in vitro assay conditions. Bridging the gap between in vitro and in vivo oxygen tensions would allow for more physiologically representative insights into viral pathogenesis.
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Affiliation(s)
- Esther Shuyi Gan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
| | - Eng Eong Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore
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35
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Pong Ng H, Kim GD, Ricky Chan E, Dunwoodie SL, Mahabeleshwar GH. CITED2 limits pathogenic inflammatory gene programs in myeloid cells. FASEB J 2020; 34:12100-12113. [PMID: 32697413 PMCID: PMC7496281 DOI: 10.1096/fj.202000864r] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/18/2020] [Accepted: 06/29/2020] [Indexed: 12/24/2022]
Abstract
Monocyte‐derived macrophages are the major innate immune cells that provide the first line of cellular defense against infections or injuries. These recruited macrophages at the site of inflammation are exposed to a broad range of cytokines that categorically incite a robust pro‐inflammatory response. However, macrophage pro‐inflammatory activation must be under exquisite control to avert unbridled inflammation. Thus, endogenous mechanisms must exist that rigorously preserve macrophage quiescence and yet, allow nimble pro‐inflammatory macrophage response with precise spatiotemporal control. Herein, we identify the CBP/p300‐interacting transactivator with glutamic acid/aspartic acid‐rich carboxyl‐terminal domain 2 (CITED2) as a critical intrinsic negative regulator of inflammation, which broadly attenuates pro‐inflammatory gene programs in macrophages. Our in vivo studies revealed that myeloid‐CITED2 deficiency significantly heightened macrophages and neutrophils recruitment to the site of inflammation. Our integrated transcriptomics and gene set enrichment analysis (GSEA) studies uncovered that CITED2 deficiency broadly enhances NFκB targets, IFNγ/IFNα responses, and inflammatory response gene expression in macrophages. Using complementary gain‐ and loss‐of‐function studies, we observed that CITED2 overexpression attenuate and CITED2 deficiency elevate LPS‐induced NFκB transcriptional activity and NFκB‐p65 recruitment to target gene promoter in macrophages. More importantly, blockade of NFκB signaling completely reversed elevated pro‐inflammatory gene expression in macrophages. Collectively, our findings show that CITED2 restrains NFκB activation and curtails broad pro‐inflammatory gene programs in myeloid cells.
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Affiliation(s)
- Hang Pong Ng
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Gun-Dong Kim
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - E Ricky Chan
- Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Sydney, Australia.,UNSW Sydney, Sydney, Australia
| | - Ganapati H Mahabeleshwar
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,Cardiovascular Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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Fernandes MT, Calado SM, Mendes-Silva L, Bragança J. CITED2 and the modulation of the hypoxic response in cancer. World J Clin Oncol 2020; 11:260-274. [PMID: 32728529 PMCID: PMC7360518 DOI: 10.5306/wjco.v11.i5.260] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/13/2020] [Accepted: 05/12/2020] [Indexed: 02/06/2023] Open
Abstract
CITED2 (CBP/p300-interacting transactivator with Glu/Asp-rich C-terminal domain, 2) is a ubiquitously expressed protein exhibiting a high affinity for the CH1 domain of the transcriptional co-activators CBP/p300, for which it competes with hypoxia-inducible factors (HIFs). CITED2 is particularly efficient in the inhibition of HIF-1α-dependent transcription in different contexts, ranging from organ development and metabolic homeostasis to tissue regeneration and immunity, being also potentially involved in various other physiological processes. In addition, CITED2 plays an important role in inhibiting HIF in some diseases, including kidney and heart diseases and type 2-diabetes. In the particular case of cancer, CITED2 either functions by promoting or suppressing cancer development depending on the context and type of tumors. For instance, CITED2 overexpression promotes breast and prostate cancers, as well as acute myeloid leukemia, while its expression is downregulated to sustain colorectal cancer and hepatocellular carcinoma. In addition, the role of CITED2 in the maintenance of cancer stem cells reveals its potential as a target in non-small cell lung carcinoma and acute myeloid leukemia, for example. But besides the wide body of evidence linking both CITED2 and HIF signaling to carcinogenesis, little data is available regarding CITED2 role as a negative regulator of HIF-1α specifically in cancer. Therefore, comprehensive studies exploring further the interactions of these two important mediators in cancer-specific models are sorely needed and this can potentially lead to the development of novel targeted therapies.
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Affiliation(s)
- Mónica T Fernandes
- School of Health, Universidade do Algarve, Campus of Gambelas, Faro 8005-139, Portugal
- Centre for Biomedical Research, Universidade do Algarve, Campus of Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Centre, Faro 8005-139, Portugal
| | - Sofia M Calado
- Centre for Biomedical Research, Universidade do Algarve, Campus of Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Centre, Faro 8005-139, Portugal
| | - Leonardo Mendes-Silva
- Centre for Biomedical Research, Universidade do Algarve, Campus of Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Centre, Faro 8005-139, Portugal
- Department of Biomedical Sciences and Medicine, Universidade do Algarve, Campus of Gambelas, Faro 8005-139, Portugal
| | - José Bragança
- Centre for Biomedical Research, Universidade do Algarve, Campus of Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Centre, Faro 8005-139, Portugal
- Department of Biomedical Sciences and Medicine, Universidade do Algarve, Campus of Gambelas, Faro 8005-139, Portugal
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Partch CL. Orchestration of Circadian Timing by Macromolecular Protein Assemblies. J Mol Biol 2020; 432:3426-3448. [DOI: 10.1016/j.jmb.2019.12.046] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/13/2019] [Accepted: 12/18/2019] [Indexed: 12/13/2022]
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Xiao S, Zhang D, Liu Z, Jin W, Huang G, Wei Z, Wang D, Deng C. Diabetes-induced glucolipotoxicity impairs wound healing ability of adipose-derived stem cells-through the miR-1248/CITED2/HIF-1α pathway. Aging (Albany NY) 2020; 12:6947-6965. [PMID: 32294623 PMCID: PMC7202540 DOI: 10.18632/aging.103053] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 03/29/2020] [Indexed: 04/13/2023]
Abstract
Despite being an attractive cell type for mesenchymal stem cell (MSC) transplantation therapy for wound healing, human adipose-derived stem cells (hADSCs) from diabetes mellitus (DM) patients result in remarkable retention of stem cell activity due to diabetes-induced glucolipotoxicity. We explored the effect of diabetes and medium containing AGEs on the cell activity, phenotype, multipotency, angiogenic potential, and the therapeutic effect of hADSCs. Then, miRNA-1248 was selected by miRNA microarray analysis to further study the core molecular pathways that regulate the wound healing ability of hADSCs. hADSCs isolated from DM patients or cultured in medium containing AGEs in vitro exhibited decreased effectiveness in stem cell therapy. The expression of miRNA-1248 was decreased in the hADSCs of DM patients and hence failed to positively regulate stem cell activity, differentiation functions, and angiogenesis promotion effect. This concomitantly increased the expression of CITED2, an inhibitor of HIF-1α, thus influencing growth factors that promote angiogenesis, cellular proliferation, and wound healing. Overall, our data demonstrated that the glucolipotoxicity-impaired wound healing ability of hADSCs might occur through the miR-1248/CITED2/HIF-1α pathway. MiRNA-1248 may have potential to be used as a novel therapeutic target for wound healing in DM patients or restoring the wound healing ability of diabetic hADSCs.
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Affiliation(s)
- Shune Xiao
- Department of Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Dan Zhang
- Department of Orthodontics, Stomatological Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Zhiyuan Liu
- Department of Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Wenhu Jin
- Department of Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Guangtao Huang
- Department of Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Zairong Wei
- Department of Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Dali Wang
- Department of Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Chengliang Deng
- Department of Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
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Investigations of the underlying mechanisms of HIF-1α and CITED2 binding to TAZ1. Proc Natl Acad Sci U S A 2020; 117:5595-5603. [PMID: 32123067 DOI: 10.1073/pnas.1915333117] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The TAZ1 domain of CREB binding protein is crucial for transcriptional regulation and recognizes multiple targets. The interactions between TAZ1 and its specific targets are related to the cellular hypoxic negative feedback regulation. Previous experiments reported that one of the TAZ1 targets, CITED2, is an efficient competitor of another target, HIF-1α. Here, by developing the structure-based models of TAZ1 complexes, we have uncovered the underlying mechanisms of the competitions between the two intrinsic disordered proteins (IDPs) HIF-1α and CITED2 binding to TAZ1. Our results support the experimental hypothesis on the competition mechanisms and the apparent affinity. Furthermore, the simulations locate the dominant position of forming TAZ1-CITED2 complex in both thermodynamics and kinetics. For thermodynamics, TAZ1-CITED2 is the lowest basin located on the free energy surface of binding in the ternary system. For kinetics, the results suggest that CITED2 binds to TAZ1 faster than HIF-1α. In addition, the analysis of contact map and Φ values is important for guiding further experimental studies to understand the biomolecular functions of IDPs.
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40
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Ruiz-Ortiz I, De Sancho D. Competitive binding of HIF-1α and CITED2 to the TAZ1 domain of CBP from molecular simulations. Phys Chem Chem Phys 2020; 22:8118-8127. [DOI: 10.1039/d0cp00328j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Many intrinsically disordered proteins (IDPs) are involved in complex signalling networks inside the cell.
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Affiliation(s)
- Irene Ruiz-Ortiz
- Donostia International Physics Center
- Donostia-San Sebastián
- Spain
| | - David De Sancho
- Donostia International Physics Center
- Donostia-San Sebastián
- Spain
- University of the Basque Country
- Faculty of Chemistry
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41
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Dianatpour S, Khatami M, Heidari MM, Hadadzadeh M. Novel Point Mutations of CITED2 Gene Are Associated with Non-familial Congenital Heart Disease (CHD) in Sporadic Pediatric Patients. Appl Biochem Biotechnol 2019; 190:896-906. [PMID: 31515672 DOI: 10.1007/s12010-019-03125-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/25/2019] [Indexed: 12/20/2022]
Abstract
CITED2 is a cardiac transcription factor that plays a critical role in cardiac development. Gene mutations in CITED2 lead to a series of cardiac malformations and congenital heart defects (CHD). Congenital heart disease generally refers to defects in the heart's structure or function and often seen in many forms such as ventricular septal defects (VSDs), atrial septal defects (ASDs), and tetralogy of Fallot (TOF). However, the mechanisms involved in these mutations are poorly understood. The aim of the present study was to evaluate the mutations of the CITED2 gene in pediatric patients with congenital heart defects. We studied the potential impact of sequence variations of the CITED2 gene in a cohort of 150 patients with non-familial CHD and 98 control individuals by polymerase chain reaction-single-stranded conformation polymorphism (PCR-SSCP) and subsequently direct sequencing. We identified seven novel CITED2 nucleotide changes. Four of these alterations were found in the coding region (c.716insG, c.389A>G, c.450G>C and c.512-538del27) and were only seen in our patients, and not detected in the control group. These mutations are leading to changes in the amino acid sequence in the position of p.Gly236fs, p.Asn125Ser, p.Gln145His, and p.Ser170-Gly178del, respectively. Other variations are located in the 5'UTR region of the gene (c.-43C>T, c.-64C>T and c.-90A>G). CITED2 gene mutations in control subjects were not observed. Our Bioinformatics assay results showed that these novel mutations alter the RNA folding, protein structure, and, therefore, probable effect on the protein function and may play a significant role in the development of congenital heart diseases.
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Affiliation(s)
- Sima Dianatpour
- Department of Biology, Faculty of Science, Yazd University, Yazd, Iran
| | - Mehri Khatami
- Department of Biology, Faculty of Science, Yazd University, Yazd, Iran.
| | | | - Mehdi Hadadzadeh
- Department of Cardiac Surgery, Afshar Hospital, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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Han J, Shao J, Chen Q, Sun H, Guan L, Li Y, Liu J, Liu H. Transcriptional changes in the hypothalamus, pituitary, and mammary gland underlying decreased lactation performance in mice under heat stress. FASEB J 2019; 33:12588-12601. [PMID: 31480864 DOI: 10.1096/fj.201901045r] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Because of climate change, heat stress (HS) causes more and more impacts on dairy animals to decrease lactation performance. The neuroendocrine system is key in regulating systemic physiological processes and milk synthesis. However, the hypothalamic-pituitary axis response to HS is still unclear. In this study, a group of lactating mice underwent a daily 2-h heat treatment (36°C) for 14 d to explore possible cross-talk between the hypothalamic-pituitary axis and mammary gland under HS. Transcriptome analyses by multitissue RNA-Seq indicated the possible mechanisms of reduced lactation performance in animals under HS. In the hypothalamus, the cAMP signaling pathway was activated to resist neuronal death, and the expression of downstream genes was increased to promote cell survival under HS. Reduced food intake might be caused by down-regulated appetite-related peptide, whereas up-regulated neuropeptide Y acted to attenuate reduced food intake. In pituitary, energy stress from lower food intake might result in reduced secretion of prolactin and growth hormone. Under HS, the mammary gland may undergo hypoxic stress, causing mammary epithelial cell apoptosis. Together, these data showed systemic changes in tissues to accommodate the effects of HS on lactation.-Han, J., Shao, J., Chen, Q., Sun, H., Guan, L., Li, Y., Liu, J., Liu, H. Transcriptional changes in the hypothalamus, pituitary, and mammary gland underlying decreased lactation performance in mice under heat stress.
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Affiliation(s)
- Jialiang Han
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China; and
| | - Juanjuan Shao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China; and
| | - Qiong Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China; and
| | - Huizeng Sun
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China; and.,Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Leluo Guan
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China; and.,Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Yongxin Li
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China; and
| | - Jianxin Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China; and
| | - Hongyun Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China; and
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Lysine acetyltransferases and lysine deacetylases as targets for cardiovascular disease. Nat Rev Cardiol 2019; 17:96-115. [DOI: 10.1038/s41569-019-0235-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/26/2019] [Indexed: 12/28/2022]
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Guo HH, Sun Y, Zhang XL, Jiang XY, Zou SM. Identification of duplicated Cited3 genes and their responses to hypoxic stress in blunt snout bream (Megalobrama amblycephala). FISH PHYSIOLOGY AND BIOCHEMISTRY 2019; 45:1141-1152. [PMID: 30963483 DOI: 10.1007/s10695-019-00625-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
The CITED3 protein is a non-DNA-binding transcriptional co-regulator involved in the regulation of various transcriptional responses against hypoxia stress. Here, we characterized two paralogs Cited3 genes (Cited3a and Cited3b) from blunt snout bream (Megalobrama amblycephala), which is a hypoxia-sensitive species. Both genes have an open reading frame of 756 and 723 bp; encoded a protein of 251 amino acid and 240 amino acid, respectively; and they shared a sequence identity of 67%. In adult fish, both Cited3a and Cited3b mRNAs were highly expressed in kidney tissues. In contrast, they were detected in the skin, muscle, and gonad at extraordinarily low levels. During embryogenesis, both Cited3a and Cited3b mRNAs were maternally deposited in eggs and fluctuated from the zygote to the 44-hpf (hours post-fertilization) larvae. Whole-mount in situ hybridization demonstrated that both Cited3a and Cited3b mRNAs were transcribed in the brain, gut, and tailbud at 12 hpf, and at the brain and gut at 24 hpf, and at the brain at 36 hpf embryos. Hypoxic treatment led to upregulated expression of the Cited3 genes during embryogenesis. Under hypoxia, both Cited3a and Cited3b genes in the kidney and brain and Cited3a genes in the liver were significantly upregulated. These results suggest that hypoxia was associated with increases in mRNA levels for both Cited3a (kidney, brain, liver) and Cited3b (kidney and liver).
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Affiliation(s)
- Hong-Hong Guo
- Genetics and Breeding Center for Blunt Snout Bream, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Yuan Sun
- Genetics and Breeding Center for Blunt Snout Bream, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Xue-Li Zhang
- Genetics and Breeding Center for Blunt Snout Bream, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Xia-Yun Jiang
- Genetics and Breeding Center for Blunt Snout Bream, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
| | - Shu-Ming Zou
- Genetics and Breeding Center for Blunt Snout Bream, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
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Role of TPBG (Trophoblast Glycoprotein) Antigen in Human Pericyte Migratory and Angiogenic Activity. Arterioscler Thromb Vasc Biol 2019; 39:1113-1124. [DOI: 10.1161/atvbaha.119.312665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Objective—
To determine the role of the oncofetal protein TPBG (trophoblast glycoprotein) in normal vascular function and reparative vascularization.
Approach and Results—
Immunohistochemistry of human veins was used to show TPBG expression in vascular smooth muscle cells and adventitial pericyte-like cells (APCs). ELISA, Western blot, immunocytochemistry, and proximity ligation assays evidenced a hypoxia-dependent upregulation of TPBG in APCs not found in vascular smooth muscle cells or endothelial cells. This involves the transcriptional modulator CITED2 (Atypical chemokine receptor 3 CBP/p300-interacting transactivator with glutamic acid (E)/aspartic acid (D)-rich tail) and downstream activation of CXCL12 (chemokine [C-X-C motif] ligand-12) signaling through the CXCR7 (C-X-C chemokine receptor type 7) receptor and ERK1/2 (extracellular signal-regulated kinases 1/2). TPBG silencing by siRNA transfection downregulated CXCL12, CXCR7, and pERK (phospho Thr202/Tyr204 ERK1/2) and reduced the APC migratory and proangiogenic capacities. TPBG forced expression induced opposite effects, which were associated with the formation of CXCR7/CXCR4 (C-X-C chemokine receptor type 4) heterodimers and could be contrasted by CXCL12 and CXCR7 neutralization. In vivo Matrigel plug assays using APCs with or without TPBG silencing evidenced TPBG is essential for angiogenesis. Finally, in immunosuppressed mice with limb ischemia, intramuscular injection of TPBG-overexpressing APCs surpassed naïve APCs in enhancing perfusion recovery and reducing the rate of toe necrosis.
Conclusions—
TPBG orchestrates the migratory and angiogenic activities of pericytes through the activation of the CXCL12/CXCR7/pERK axis. This novel mechanism could be a relevant target for therapeutic improvement of reparative angiogenesis.
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Berlow RB, Martinez-Yamout MA, Dyson HJ, Wright PE. Role of Backbone Dynamics in Modulating the Interactions of Disordered Ligands with the TAZ1 Domain of the CREB-Binding Protein. Biochemistry 2019; 58:1354-1362. [PMID: 30775911 DOI: 10.1021/acs.biochem.8b01290] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The intrinsically disordered transactivation domains of HIF-1α and CITED2 compete for binding of the TAZ1 domain of the CREB-binding protein by a unidirectional allosteric mechanism involving direct competition for shared binding sites, ternary complex formation, and TAZ1 conformational changes. To gain insight into the mechanism by which CITED2 displaces HIF-1α from TAZ1, we used nuclear magnetic resonance spin relaxation methods to obtain an atomic-level description of the picosecond to nanosecond backbone dynamics that contribute to TAZ1 binding and competition. We show that HIF-1α and CITED2 adopt different dynamics in their complexes with TAZ1, with flexibility observed for HIF-1α in regions that would maintain accessibility for CITED2 to bind to TAZ1 and facilitate subsequent HIF-1α dissociation. In contrast, critical regions of CITED2 adopt a rigid structure in its complex with TAZ1, minimizing the ability of HIF-1α to compete for binding. We also find that TAZ1, previously thought to be a rigid scaffold for binding of disordered protein ligands, displays altered backbone dynamics in its various bound states. TAZ1 is more rigid in its CITED2-bound state than in its free state or in complex with HIF-1α, with increased rigidity observed not only in the CITED2 binding site but also in regions of TAZ1 that undergo conformational changes between the HIF-1α- and CITED2-bound structures. Taken together, these data suggest that backbone dynamics in TAZ1, as well as in the HIF-1α and CITED2 ligands, play a role in modulating the occupancy of TAZ1 and highlight the importance of characterizing both binding partners in molecular interactions.
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Affiliation(s)
- Rebecca B Berlow
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Maria A Martinez-Yamout
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
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Boldt ABW, van Tong H, Grobusch MP, Kalmbach Y, Dzeing Ella A, Kombila M, Meyer CG, Kun JFJ, Kremsner PG, Velavan TP. The blood transcriptome of childhood malaria. EBioMedicine 2019; 40:614-625. [PMID: 30638864 PMCID: PMC6412103 DOI: 10.1016/j.ebiom.2018.12.055] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 12/29/2022] Open
Abstract
Background Transcriptomic research of blood cell lineages supports the understanding of distinct features of the immunopathology in human malaria. Methods We used microarray hybridization, validated by real-time RT-PCR to analyze whole blood gene expression in healthy Gabonese children and children with various conditions of Plasmodium falciparum infection, including i) asymptomatic infection, ii) uncomplicated malaria, iii) malaria associated with severe anemia and iv) cerebral malaria. Findings Our data indicate that the expression profile of 22 genes significantly differed among the investigated groups. Immunoglobulin production, complement regulation and IFN beta signaling, in particular IRF7 and ISRE binding signatures in the corresponding genes, were most conspicuous. Down-regulation in cerebral malaria seems to rely on AhRF, GABP and HIF1 hypoxia transcription factors. ARG1, BPI, CD163, IFI27, HP and TNFAIP6 transcript levels correlated positively with lactatemia, and negatively with hemoglobin concentrations. Interpretation Differences in gene expression profile reflect distinct immunopathological mechanisms of P. falciparum infection. They emerge as potential prognostic markers for early therapeutic measures and need to be validated further. Fund This work was supported by a grant of the NGFN (Nationales Genomforschungsnetz 01GS0114) and by a CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil) PhD scholarship for A. B. W. Boldt. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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Affiliation(s)
- Angelica B W Boldt
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany; Laboratory of Human Molecular Genetics, Department of Genetics, Universidade Federal do Paraná, Curitiba, Brazil.
| | - Hoang van Tong
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany; Institute of Biomedicine and Pharmacy, Vietnam Military Medical University, Hanoi, Viet Nam
| | - Martin P Grobusch
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany; Center of Medical Research Lambaréné, Lambaréné, Gabon; Center of Travel Medicine and Tropical Medicine, Department of Infectious Diseases, Division of Internal Medicine, Academic Medical Center, Amsterdam University Medical Centers, the Netherlands
| | - Yvonne Kalmbach
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Arnaud Dzeing Ella
- Department of Parasitology, Tropical Medicine and Mycology, University of Libreville, Libreville, Gabon
| | - Maryvonne Kombila
- Department of Parasitology, Tropical Medicine and Mycology, University of Libreville, Libreville, Gabon
| | - Christian G Meyer
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany; Vietnamese-German Center for Medical Research, Hanoi, Viet Nam; Duy Tan University, Da Nang, Viet Nam
| | - Jürgen F J Kun
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Peter G Kremsner
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany; Center of Medical Research Lambaréné, Lambaréné, Gabon
| | - Thirumalaisamy P Velavan
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany; Vietnamese-German Center for Medical Research, Hanoi, Viet Nam; Duy Tan University, Da Nang, Viet Nam.
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HPV-Mediated Resistance to TNF and TRAIL Is Characterized by Global Alterations in Apoptosis Regulatory Factors, Dysregulation of Death Receptors, and Induction of ROS/RNS. Int J Mol Sci 2019; 20:ijms20010198. [PMID: 30625987 PMCID: PMC6337392 DOI: 10.3390/ijms20010198] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 12/23/2018] [Accepted: 12/29/2018] [Indexed: 02/07/2023] Open
Abstract
Persistent infection with high-risk human papilloma virus (HR-HPV) is the main risk factor for the development of invasive cervical cancer although is not sufficient to cause cervical cancer. Several host and environmental factors play a key role in cancer initiation/progression, including cytokines and other immune-response mediators. Here, we characterized the response to the individual and combined action of the pro-inflammatory cytokines tumor necrosis factor (TNF) and TNF-related apoptosis-inducing ligand (TRAIL) on HPV-transformed cells and human keratinocytes ectopically expressing E6 and E7 early proteins from different HPV types. We showed that keratinocytes expressing HPV early proteins exhibited global alterations in the expression of proteins involved in apoptosis regulation/execution, including TNF and TRAIL receptors. Besides, we provided evidence that TNF receptor 1 (TNFR1) was down-regulated and may be retained in the cytoplasm of keratinocytes expressing HPV16 oncoproteins. Finally, fluorescence analysis demonstrated that cytokine treatment induced the production and release of reactive oxygen and nitrogen species (ROS/RNS) in cells expressing HPV oncogenes. Alterations in ROS/RNS production and apoptosis regulatory factors expression in response to inflammatory mediators may favor the accumulation of genetic alterations in HPV-infected cells. Altogether, our results suggested that these events may contribute to lesion progression and cancer onset.
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Soares MJ, Iqbal K, Kozai K. Hypoxia and Placental Development. Birth Defects Res 2018; 109:1309-1329. [PMID: 29105383 DOI: 10.1002/bdr2.1135] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 09/04/2017] [Indexed: 12/17/2022]
Abstract
Hemochorial placentation is orchestrated through highly regulated temporal and spatial decisions governing the fate of trophoblast stem/progenitor cells. Trophoblast cell acquisition of specializations facilitating invasion and uterine spiral artery remodeling is a labile process, sensitive to the environment, and represents a process that is vulnerable to dysmorphogenesis in pathologic states. Hypoxia is a signal guiding placental development, and molecular mechanisms directing cellular adaptations to low oxygen tension are integral to trophoblast cell differentiation and placentation. Hypoxia can also be used as an experimental tool to investigate regulatory processes controlling hemochorial placentation. These developmental processes are conserved in mouse, rat, and human placentation. Consequently, elements of these developmental events can be modeled and hypotheses tested in trophoblast stem cells and in genetically manipulated rodents. Hypoxia is also a consequence of a failed placenta, yielding pathologies that can adversely affect maternal adjustments to pregnancy, fetal health, and susceptibility to adult disease. The capacity of the placenta for adaptation to environmental challenges highlights the importance of its plasticity in safeguarding a healthy pregnancy. Birth Defects Research 109:1309-1329, 2017.© 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Michael J Soares
- Institute for Reproduction and Perinatal Research, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas.,Department of Pediatrics, University of Kansas Medical Center, Kansas City, Kansas.,Fetal Health Research, Children's Research Institute, Children's Mercy, Kansas City, Missouri
| | - Khursheed Iqbal
- Institute for Reproduction and Perinatal Research, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Keisuke Kozai
- Institute for Reproduction and Perinatal Research, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
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AlAbdi L, He M, Yang Q, Norvil AB, Gowher H. The transcription factor Vezf1 represses the expression of the antiangiogenic factor Cited2 in endothelial cells. J Biol Chem 2018; 293:11109-11118. [PMID: 29794136 PMCID: PMC6052231 DOI: 10.1074/jbc.ra118.002911] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/19/2018] [Indexed: 01/05/2023] Open
Abstract
Formation of the vasculature by angiogenesis is critical for proper development, but angiogenesis also contributes to the pathogenesis of various disorders, including cancer and cardiovascular diseases. Vascular endothelial zinc finger 1 (Vezf1), is a Krüppel-like zinc finger protein that plays a vital role in vascular development. However, the mechanism by which Vezf1 regulates this process is not fully understood. Here, we show that Vezf1−/− mouse embryonic stem cells (ESC) have significantly increased expression of a stem cell factor, Cbp/p300-interacting transactivator 2 (Cited2). Compared with WT ESCs, Vezf1−/− ESCs inefficiently differentiated into endothelial cells (ECs), which exhibited defects in the tube-formation assay. These defects were due to reduced activation of EC-specific genes concomitant with lower enrichment of histone 3 acetylation at Lys27 (H3K27) at their promoters. We hypothesized that overexpression of Cited2 in Vezf1−/− cells sequesters P300/CBP away from the promoters of proangiogenic genes and thereby contributes to defective angiogenesis in these cells. This idea was supported by the observation that shRNA-mediated depletion of Cited2 significantly reduces the angiogenic defects in the Vezf1−/− ECs. In contrast to previous studies that have focused on the role of Vezf1 as a transcriptional activator of proangiogenic genes, our findings have revealed a role for Vezf1 in modulating the expression of the antiangiogenic factor Cited2. Vezf1 previously has been characterized as an insulator protein, and our results now provide insights into the mechanism, indicating that Vezf1 can block inappropriate, nonspecific interactions of promoters with cis-located enhancers, preventing aberrant promoter activation.
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Affiliation(s)
| | - Ming He
- From the Department of Biochemistry and
| | | | | | - Humaira Gowher
- From the Department of Biochemistry and .,Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
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